RetrogeneDB ID: retro_nleu_335

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397263.1:52157782..52158211(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PPP1R14B
• Ensembl ID: ENSNLEG00000004890
• Aliases: None
• Description: None

Sequence

>retro_nleu_335
GGCGGCCGCCGTGGCGGACAGCTGCAGCGCGAGGGGCGCGGCGTTGGCTACCCCGGCCCGGGACCACGCGTCTACTTTCA
GAGACCCGCCGGGGCCGCAGGAGAGAGCCCGGGCGGCGCGGACGATGAGGGCCCAGTGAGGCGCCAAGTGAAGGTCACCG
TCAAGTATGACCGCAAGGAGCTACGGAAGCGCCTCAACCTAGAGGAGTAGATCCTGGAGCAGCTCACGCGCCTCTACGAC
TGCCAGGAAGAGGAGATCCGAGAACTGGAGATTGACGTGGATGAGCTCCTGGACATGGAGAGTGACGATGCCCAGGCTGC
CAGGGTCAAGGAGCTGCTGGTTGACTATTACAAACCCACAGAAGCCTTCATCTCTGGCCTGCTGGACAAGATCCGGGGCA
TGCAGAAGCTGAGCACACCGCAGAAGAAG

Alignment

ORF - retro_nleu_335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.31 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTAGGAALAAPAPGPGSGGPGPRVYFQSPPGAAGEGPGGADDEGPVRRQGKVTVKYDRKELRKRLNLEEW
          G...G..L.....G.G..GPGPRVYFQ.P.GAAGE.PGGADDEGPVRRQ.KVTVKYDRKELRKRLNLEE.
Retrocopy GGRRGGQLQREGRGVGYPGPGPRVYFQRPAGAAGESPGGADDEGPVRRQVKVTVKYDRKELRKRLNLEE*

Parental  ILEQLTRLYDCQEEEIPELEIDVDELLDMESDDARAARVKELLVDCYKPTEAFISGLLDKIRGMQKLSTP
          ILEQLTRLYDCQEEEI.ELEIDVDELLDMESDDA.AARVKELLVD.YKPTEAFISGLLDKIRGMQKLSTP
Retrocopy ILEQLTRLYDCQEEEIRELEIDVDELLDMESDDAQAARVKELLVDYYKPTEAFISGLLDKIRGMQKLSTP

Parental  QKK
          QKK
Retrocopy QKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_335 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018111	3 retrocopies	retro_cjac_3591, retro_cjac_428, retro_cjac_532,
Homo sapiens	ENSG00000173457	4 retrocopies	retro_hsap_2205, retro_hsap_3101, retro_hsap_3655, retro_hsap_3838,
Mustela putorius furo	ENSMPUG00000013208	2 retrocopies	retro_mputfur_235, retro_mputfur_798,
Nomascus leucogenys	ENSNLEG00000004890	2 retrocopies	retro_nleu_324, retro_nleu_335 ,
Pan troglodytes	ENSPTRG00000041138	6 retrocopies	retro_ptro_1674, retro_ptro_2097, retro_ptro_2480, retro_ptro_2614, retro_ptro_3089, retro_ptro_935,
Sus scrofa	ENSSSCG00000013035	2 retrocopies	retro_sscr_1087, retro_sscr_892,
Ictidomys tridecemlineatus	ENSSTOG00000021959	1 retrocopy	retro_itri_1110,